table of contents
g_tune_pme(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_tune_pme(1) |
NAME¶
g_tune_pme - time mdrun as a function of PME nodes to optimize settingsSYNOPSIS¶
g_tune_pme -p perf.out -err errors.log -so tuned.tpr -s topol.tpr -o traj.trr -x traj.xtc -cpi state.cpt -cpo state.cpt -c confout.gro -e ener.edr -g md.log -dhdl dhdl.xvg -field field.xvg -table table.xvg -tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei sam.edi -eo sam.edo -j wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav runaver.xvg -px pullx.xvg -pf pullf.xvg -mtx nm.mtx -dn dipole.ndx -bo bench.trr -bx bench.xtc -bcpo bench.cpt -bc bench.gro -be bench.edr -bg bench.log -beo bench.edo -bdhdl benchdhdl.xvg -bfield benchfld.xvg -btpi benchtpi.xvg -btpid benchtpid.xvg -bjo bench.gct -bffout benchgct.xvg -bdevout benchdev.xvg -brunav benchrnav.xvg -bpx benchpx.xvg -bpf benchpf.xvg -bmtx benchn.mtx -bdn bench.ndx -[no]h -[no]version -nice int -xvg enum -np int -npstring enum -nt int -r int -max real -min real -npme enum -fix int -upfac real -downfac real -ntpr int -four real -steps step -resetstep int -simsteps step -[no]launch -deffnm string -ddorder enum -[no]ddcheck -rdd real -rcon real -dlb enum -dds real -gcom int -[no]v -[no]compact -[no]seppot -pforce real -[no]reprod -cpt real -[no]cpnum -[no]append -maxh real -multi int -replex int -reseed int -[no]ionizeDESCRIPTION¶
For a given number -np or -nt of processors/threads, this program systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It will also test whether performance can be enhanced by shifting load from the reciprocal to the real space part of the Ewald sum. Simply pass your .tpr file to g_tune_pme together with other options for mdrun as needed.FILES¶
-p perf.out OutputGeneric output file
Log file
Run input file: tpr tpb tpa
Run input file: tpr tpb tpa
Full precision trajectory: trr trj cpt
Compressed trajectory (portable xdr format)
Checkpoint file
Checkpoint file
Structure file: gro g96 pdb etc.
Energy file
Log file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Trajectory: xtc trr trj gro g96 pdb cpt
xvgr/xmgr file
xvgr/xmgr file
ED sampling input
ED sampling output
General coupling stuff
General coupling stuff
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Hessian matrix
Index file
Full precision trajectory: trr trj cpt
Compressed trajectory (portable xdr format)
Checkpoint file
Structure file: gro g96 pdb etc.
Energy file
Log file
ED sampling output
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
General coupling stuff
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Hessian matrix
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
xvg plot formatting: xmgrace, xmgr or none
Number of nodes to run the tests on (must be 2 for separate PME nodes)
Specify the number of processors to $MPIRUN using this string: -np, -n or none
Number of threads to run the tests on (turns MPI & mpirun off)
Repeat each test this often
Max fraction of PME nodes to test with
Min fraction of PME nodes to test with
Benchmark all possible values for -npme or just the subset that is expected to perform well: auto, all or subset
If = -1, do not vary the number of PME-only nodes, instead use this fixed value and only vary rcoulomb and the PME grid spacing.
Upper limit for rcoulomb scaling factor (Note that rcoulomb upscaling results in fourier grid downscaling)
Lower limit for rcoulomb scaling factor
Number of .tpr files to benchmark. Create this many files with scaling factors ranging from 1.0 to fac. If 1, automatically choose the number of .tpr files to test
Use this fourierspacing value instead of the grid found in the .tpr input file. (Spacing applies to a scaling factor of 1.0 if multiple .tpr files are written)
Take timings for this many steps in the benchmark runs
Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)
If non-negative, perform this many steps in the real run (overwrites nsteps from .tpr, add .cpt steps)
Launch the real simulation after optimization
Set the default filename for all file options at launch time
DD node order: interleave, pp_pme or cartesian
Check for all bonded interactions with DD
The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates
Maximum distance for P-LINCS (nm), 0 is estimate
Dynamic load balancing (with DD): auto, no or yes
Minimum allowed dlb scaling of the DD cell size
Global communication frequency
Be loud and noisy
Write a compact log file
Write separate V and dVdl terms for each interaction type and node to the log file(s)
Print all forces larger than this (kJ/mol nm)
Try to avoid optimizations that affect binary reproducibility
Checkpoint interval (minutes)
Keep and number checkpoint files
Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only)
Terminate after 0.99 times this time (hours)
Do multiple simulations in parallel
Attempt replica exchange every steps
Seed for replica exchange, -1 is generate a seed
Do a simulation including the effect of an X-ray bombardment on your system
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |